Starting phenix.real_space_refine
on Sat Jul 26 08:35:45 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9jjk_61530/07_2025/9jjk_61530.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jjk_61530/07_2025/9jjk_61530.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jjk_61530/07_2025/9jjk_61530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jjk_61530/07_2025/9jjk_61530.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jjk_61530/07_2025/9jjk_61530.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jjk_61530/07_2025/9jjk_61530.cif"
  }
  resolution = 2.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.064
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      63      5.16       5
     C    5382      2.51       5
     N    1421      2.21       5
     O    1491      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8358
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1048, 8250
          Classifications: {'peptide': 1048}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 54, 'TRANS': 993}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.59, per 1000 atoms: 0.67
  Number of scatterers: 8358
  At special positions: 0
  Unit cell: (73.87, 90.47, 166.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     P       1     15.00
     O    1491      8.00
     N    1421      7.00
     C    5382      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A1202 "
      " NAG C   1 " - " ASN A1205 "
  Time building additional restraints: 2.47
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1990

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      58.2% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 44
      removed outlier: 3.650A  pdb=" N   CYS A  44 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 53
    Processing helix  chain 'A' and resid 66 through 83
      removed outlier: 3.550A  pdb=" N   ALA A  70 " --> pdb=" O   HIS A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 122
      removed outlier: 3.608A  pdb=" N   VAL A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ARG A 122 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 140
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 249 through 260
      removed outlier: 4.481A  pdb=" N   ASN A 253 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 302
      removed outlier: 4.346A  pdb=" N   VAL A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 309 through 323
      removed outlier: 5.185A  pdb=" N   GLN A 318 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 326
      No H-bonds generated for 'chain 'A' and resid 324 through 326'
    Processing helix  chain 'A' and resid 329 through 350
      removed outlier: 3.746A  pdb=" N   SER A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 391
    Processing helix  chain 'A' and resid 402 through 408
    Processing helix  chain 'A' and resid 578 through 594
      removed outlier: 3.644A  pdb=" N   LEU A 582 " --> pdb=" O   HIS A 578 " (cutoff:3.500A)
      Proline residue:  A 584  - end of helix
    Processing helix  chain 'A' and resid 595 through 616
      removed outlier: 3.833A  pdb=" N   ARG A 601 " --> pdb=" O   SER A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 638
      removed outlier: 3.598A  pdb=" N   ALA A 634 " --> pdb=" O   LEU A 630 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 638 " --> pdb=" O   ALA A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 645
    Processing helix  chain 'A' and resid 705 through 712
      removed outlier: 3.552A  pdb=" N   GLU A 711 " --> pdb=" O   ASP A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 744
      removed outlier: 3.726A  pdb=" N   SER A 743 " --> pdb=" O   ARG A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 763
    Processing helix  chain 'A' and resid 814 through 819
      removed outlier: 3.682A  pdb=" N   LEU A 818 " --> pdb=" O   CYS A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 847
    Processing helix  chain 'A' and resid 858 through 869
      removed outlier: 3.665A  pdb=" N   LYS A 868 " --> pdb=" O   VAL A 864 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 956
      No H-bonds generated for 'chain 'A' and resid 954 through 956'
    Processing helix  chain 'A' and resid 957 through 965
    Processing helix  chain 'A' and resid 967 through 971
    Processing helix  chain 'A' and resid 979 through 993
    Processing helix  chain 'A' and resid 1005 through 1007
      No H-bonds generated for 'chain 'A' and resid 1005 through 1007'
    Processing helix  chain 'A' and resid 1008 through 1015
    Processing helix  chain 'A' and resid 1050 through 1060
    Processing helix  chain 'A' and resid 1071 through 1073
      No H-bonds generated for 'chain 'A' and resid 1071 through 1073'
    Processing helix  chain 'A' and resid 1074 through 1113
    Processing helix  chain 'A' and resid 1120 through 1138
      Proline residue:  A1133  - end of helix
      removed outlier: 3.618A  pdb=" N   SER A1138 " --> pdb=" O   LEU A1134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1139 through 1141
      No H-bonds generated for 'chain 'A' and resid 1139 through 1141'
    Processing helix  chain 'A' and resid 1147 through 1151
      removed outlier: 3.845A  pdb=" N   MET A1151 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1161 through 1201
      removed outlier: 3.529A  pdb=" N   GLN A1165 " --> pdb=" O   PRO A1161 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   LEU A1178 " --> pdb=" O   LEU A1174 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   THR A1179 " --> pdb=" O   LYS A1175 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ARG A1199 " --> pdb=" O   CYS A1195 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP A1200 " --> pdb=" O   ASP A1196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1225 through 1251
      removed outlier: 3.530A  pdb=" N   LEU A1230 " --> pdb=" O   ALA A1226 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   THR A1250 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1265
      removed outlier: 3.751A  pdb=" N   THR A1265 " --> pdb=" O   SER A1262 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1262 through 1265'
    Processing helix  chain 'A' and resid 1266 through 1291
      Proline residue:  A1274  - end of helix
    Processing helix  chain 'A' and resid 1301 through 1305
      removed outlier: 3.897A  pdb=" N   VAL A1305 " --> pdb=" O   LEU A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1348
      removed outlier: 3.838A  pdb=" N   TRP A1310 " --> pdb=" O   PRO A1306 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   VAL A1321 " --> pdb=" O   LEU A1317 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   VAL A1322 " --> pdb=" O   VAL A1318 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR A1323 " --> pdb=" O   LEU A1319 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ARG A1337 " --> pdb=" O   ARG A1333 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 178
      removed outlier: 4.349A  pdb=" N   TRP A 167 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   ILE A 187 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG A 241 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 879 through 880
      removed outlier: 6.604A  pdb=" N   ILE A 879 " --> pdb=" O   THR A 976 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   PHE A 975 " --> pdb=" O   PHE A 851 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   TYR A 853 " --> pdb=" O   PHE A 975 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   LEU A 413 " --> pdb=" O   VAL A 852 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   PHE A 854 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   CYS A 415 " --> pdb=" O   PHE A 854 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   THR A 997 " --> pdb=" O   ILE A1017 " (cutoff:3.500A)
      removed outlier: 8.196A  pdb=" N   ILE A1019 " --> pdb=" O   THR A 997 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   CYS A 999 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   LEU A1021 " --> pdb=" O   CYS A 999 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   GLY A1001 " --> pdb=" O   LEU A1021 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   SER A1018 " --> pdb=" O   LEU A1065 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   PHE A1067 " --> pdb=" O   SER A1018 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ALA A1020 " --> pdb=" O   PHE A1067 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 552 through 557
      removed outlier: 6.011A  pdb=" N   GLN A 830 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR A 431 " --> pdb=" O   SER A 828 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   GLY A 825 " --> pdb=" O   PHE A 749 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   PHE A 749 " --> pdb=" O   GLY A 825 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   VAL A 827 " --> pdb=" O   SER A 747 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   SER A 702 " --> pdb=" O   ALA A 750 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS A 752 " --> pdb=" O   MET A 700 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   SER A 683 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   LYS A 691 " --> pdb=" O   GLN A 649 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   GLN A 649 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 9.004A  pdb=" N   ILE A 767 " --> pdb=" O   HIS A 652 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ALA A 654 " --> pdb=" O   ILE A 767 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   LEU A 769 " --> pdb=" O   ALA A 654 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   TYR A 656 " --> pdb=" O   LEU A 769 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 559 through 560
    Processing sheet with id=AA5, first strand: chain 'A' and resid 722 through 724
      removed outlier: 5.803A  pdb=" N   GLN A 821 " --> pdb=" O   CYS A 713 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 756 through 757

    467 hydrogen bonds defined for protein.
    1350 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.87

  Time building geometry restraints manager: 2.89 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.33: 1561
        1.33 -     1.45: 2036
        1.45 -     1.58: 4860
        1.58 -     1.70: 2
        1.70 -     1.82: 85
  Bond restraints: 8544
  Sorted by residual:
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.498 -0.092 2.00e-02 2.50e+03 2.12e+01
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.32e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.441 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.51e+00
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.27e+00
  ... (remaining 8539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 11488
        2.38 -     4.77: 104
        4.77 -     7.15: 6
        7.15 -     9.54: 0
        9.54 -    11.92: 3
  Bond angle restraints: 11601
  Sorted by residual:
  angle pdb=" CB  MET A 826 "
        pdb=" CG  MET A 826 "
        pdb=" SD  MET A 826 "
      ideal   model   delta    sigma   weight residual
     112.70  124.62  -11.92 3.00e+00 1.11e-01 1.58e+01
  angle pdb=" CB  MET A 378 "
        pdb=" CG  MET A 378 "
        pdb=" SD  MET A 378 "
      ideal   model   delta    sigma   weight residual
     112.70  123.47  -10.77 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" CA  LEU A 602 "
        pdb=" CB  LEU A 602 "
        pdb=" CG  LEU A 602 "
      ideal   model   delta    sigma   weight residual
     116.30  126.19   -9.89 3.50e+00 8.16e-02 7.98e+00
  angle pdb=" N   VAL A1113 "
        pdb=" CA  VAL A1113 "
        pdb=" C   VAL A1113 "
      ideal   model   delta    sigma   weight residual
     112.80  109.76    3.04 1.15e+00 7.56e-01 6.99e+00
  angle pdb=" C   CYS A1131 "
        pdb=" N   TYR A1132 "
        pdb=" CA  TYR A1132 "
      ideal   model   delta    sigma   weight residual
     121.80  115.39    6.41 2.44e+00 1.68e-01 6.89e+00
  ... (remaining 11596 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.40: 4592
       22.40 -    44.79: 471
       44.79 -    67.19: 103
       67.19 -    89.59: 11
       89.59 -   111.98: 12
  Dihedral angle restraints: 5189
    sinusoidal: 2142
      harmonic: 3047
  Sorted by residual:
  dihedral pdb=" C1  NAG B   1 "
           pdb=" C5  NAG B   1 "
           pdb=" O5  NAG B   1 "
           pdb=" C4  NAG B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   47.87 -111.98     1      3.00e+01 1.11e-03 1.47e+01
  dihedral pdb=" C1  NAG B   1 "
           pdb=" C5  NAG B   1 "
           pdb=" O5  NAG B   1 "
           pdb=" C6  NAG B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -77.36 -111.48     1      3.00e+01 1.11e-03 1.46e+01
  dihedral pdb=" CA  ASN A1202 "
           pdb=" C   ASN A1202 "
           pdb=" N   LEU A1203 "
           pdb=" CA  LEU A1203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.13  -18.87     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 5186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1288
       0.078 -    0.156: 79
       0.156 -    0.234: 0
       0.234 -    0.311: 0
       0.311 -    0.389: 1
  Chirality restraints: 1368
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A1202 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CA  TRP A  67 "
            pdb=" N   TRP A  67 "
            pdb=" C   TRP A  67 "
            pdb=" CB  TRP A  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.67e-01
  chirality pdb=" CA  ASN A 876 "
            pdb=" N   ASN A 876 "
            pdb=" C   ASN A 876 "
            pdb=" CB  ASN A 876 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.49e-01
  ... (remaining 1365 not shown)

  Planarity restraints: 1442
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 313 "    0.016 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   THR A 313 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   THR A 313 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A 314 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1128 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.27e+00
        pdb=" C   SER A1128 "    0.050 2.00e-02 2.50e+03
        pdb=" O   SER A1128 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   CYS A1129 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A1202 "    0.023 2.00e-02 2.50e+03   2.13e-02 5.68e+00
        pdb=" CG  ASN A1202 "   -0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASN A1202 "    0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A1202 "   -0.019 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1439 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1642
        2.78 -     3.31: 7336
        3.31 -     3.84: 13494
        3.84 -     4.37: 15372
        4.37 -     4.90: 27496
  Nonbonded interactions: 65340
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 207 "
            pdb=" OE1 GLU A 207 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   LEU A1288 "
            pdb=" OG1 THR A1292 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ALA A 613 "
            pdb=" OG  SER A 617 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG1 THR A 580 "
            pdb=" O   GLY A 719 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" NH2 ARG A  20 "
            pdb=" O   ARG A 143 "
     model   vdw
     2.347 3.120
  ... (remaining 65335 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     25.300
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092   8548  Z= 0.142
  Angle     :  0.562  11.924  11613  Z= 0.277
  Chirality :  0.039   0.389   1368
  Planarity :  0.005   0.057   1440
  Dihedral  : 18.955 111.983   3199
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 22.73 %
    Favored  : 73.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.27), residues: 1030
  helix:  2.80 (0.23), residues: 536
  sheet:  0.69 (0.46), residues: 112
  loop : -0.06 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A1253 
 PHE   0.013   0.001   PHE A1093 
 TYR   0.018   0.001   TYR A1087 
 ARG   0.004   0.000   ARG A 601 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01467 (    2)
  link_NAG-ASN         : angle       3.84723 (    6)
  link_BETA1-4         : bond        0.00798 (    2)
  link_BETA1-4         : angle       2.17420 (    6)
  hydrogen bonds       : bond        0.18273 (  467)
  hydrogen bonds       : angle       5.29934 ( 1350)
  covalent geometry    : bond        0.00280 ( 8544)
  covalent geometry    : angle       0.55307 (11601)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
REVERT: A 1260 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7461 (mtt90)
  outliers start: 38
  outliers final: 33
  residues processed: 118
  average time/residue: 1.2205
  time to fit residues: 154.2902
Evaluate side-chains
  116 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 82
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  208 HIS
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue 1017 ILE
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1064 SER
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1127 LEU
Chi-restraints excluded: chain A residue 1155 LYS
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1256 LYS
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain A residue 1320 VAL
Chi-restraints excluded: chain A residue 1323 THR
Chi-restraints excluded: chain A residue 1347 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.179321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.105152 restraints weight = 8123.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 3.96
r_work: 0.2955 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.0914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8548  Z= 0.200
  Angle     :  0.686  10.797  11613  Z= 0.338
  Chirality :  0.044   0.214   1368
  Planarity :  0.005   0.051   1440
  Dihedral  : 12.943  84.849   1304
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 19.96 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.26), residues: 1030
  helix:  2.31 (0.22), residues: 555
  sheet:  0.44 (0.46), residues: 117
  loop : -0.29 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 310 
 HIS   0.004   0.001   HIS A 405 
 PHE   0.023   0.002   PHE A1093 
 TYR   0.015   0.002   TYR A 312 
 ARG   0.002   0.000   ARG A 129 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00848 (    2)
  link_NAG-ASN         : angle       3.35577 (    6)
  link_BETA1-4         : bond        0.00559 (    2)
  link_BETA1-4         : angle       2.44333 (    6)
  hydrogen bonds       : bond        0.09439 (  467)
  hydrogen bonds       : angle       4.32280 ( 1350)
  covalent geometry    : bond        0.00466 ( 8544)
  covalent geometry    : angle       0.67955 (11601)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 79
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8145 (mp)
REVERT: A  186 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8218 (t0)
REVERT: A  280 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7985 (mmm)
REVERT: A  344 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7563 (mtp180)
REVERT: A  826 MET cc_start: 0.5371 (mmm) cc_final: 0.5133 (mmm)
REVERT: A 1000 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8292 (mp)
REVERT: A 1225 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.8018 (m-80)
  outliers start: 55
  outliers final: 30
  residues processed: 121
  average time/residue: 1.2457
  time to fit residues: 160.8984
Evaluate side-chains
  114 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 78
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  982 THR
Chi-restraints excluded: chain A residue  988 LYS
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1127 LEU
Chi-restraints excluded: chain A residue 1155 LYS
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1295 ASP
Chi-restraints excluded: chain A residue 1347 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0870
   chunk 56 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 36 optimal weight:    0.1980
   chunk 82 optimal weight:    0.4980
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.5158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 830 GLN
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.183914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.113265 restraints weight = 8221.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 3.48
r_work: 0.3030 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.0891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8548  Z= 0.125
  Angle     :  0.543   8.228  11613  Z= 0.272
  Chirality :  0.039   0.248   1368
  Planarity :  0.005   0.055   1440
  Dihedral  : 10.523  83.230   1282
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 21.56 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.27), residues: 1030
  helix:  2.69 (0.22), residues: 550
  sheet:  0.49 (0.46), residues: 112
  loop : -0.03 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 310 
 HIS   0.003   0.000   HIS A 608 
 PHE   0.017   0.001   PHE A 736 
 TYR   0.008   0.001   TYR A 737 
 ARG   0.002   0.000   ARG A1201 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00635 (    2)
  link_NAG-ASN         : angle       3.11222 (    6)
  link_BETA1-4         : bond        0.00238 (    2)
  link_BETA1-4         : angle       2.18080 (    6)
  hydrogen bonds       : bond        0.06510 (  467)
  hydrogen bonds       : angle       4.03048 ( 1350)
  covalent geometry    : bond        0.00243 ( 8544)
  covalent geometry    : angle       0.53602 (11601)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 82
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6435 (ttmt)
REVERT: A   78 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8354 (mp)
REVERT: A  555 MET cc_start: 0.4554 (ppp) cc_final: 0.4305 (ppp)
REVERT: A 1000 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8398 (mp)
REVERT: A 1070 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7076 (pm20)
REVERT: A 1225 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7828 (m-80)
  outliers start: 42
  outliers final: 21
  residues processed: 117
  average time/residue: 1.1914
  time to fit residues: 149.4784
Evaluate side-chains
  101 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1070 GLU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1318 VAL
Chi-restraints excluded: chain A residue 1347 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 85 optimal weight:    0.0770
   chunk 41 optimal weight:   20.0000
   chunk 69 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 101 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 44 optimal weight:    8.9990
   chunk 92 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.8740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.181869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.115532 restraints weight = 8162.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.00
r_work: 0.2995 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.0980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8548  Z= 0.139
  Angle     :  0.561   7.829  11613  Z= 0.281
  Chirality :  0.039   0.204   1368
  Planarity :  0.005   0.050   1440
  Dihedral  :  9.833  86.350   1269
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 21.34 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.27), residues: 1030
  helix:  2.67 (0.22), residues: 550
  sheet:  0.32 (0.46), residues: 112
  loop : -0.06 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A1253 
 PHE   0.019   0.001   PHE A1093 
 TYR   0.012   0.001   TYR A 312 
 ARG   0.001   0.000   ARG A1254 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00637 (    2)
  link_NAG-ASN         : angle       2.61326 (    6)
  link_BETA1-4         : bond        0.00449 (    2)
  link_BETA1-4         : angle       2.15116 (    6)
  hydrogen bonds       : bond        0.07244 (  467)
  hydrogen bonds       : angle       4.07205 ( 1350)
  covalent geometry    : bond        0.00293 ( 8544)
  covalent geometry    : angle       0.55561 (11601)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 80
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6411 (ttmt)
REVERT: A   48 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6929 (mptt)
REVERT: A   78 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8394 (mp)
REVERT: A  344 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7771 (mtp180)
REVERT: A  403 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8428 (mp)
REVERT: A 1000 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8417 (mp)
REVERT: A 1225 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7821 (m-80)
REVERT: A 1260 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7660 (mtp85)
REVERT: A 1294 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7682 (mmp80)
REVERT: A 1342 GLN cc_start: 0.8203 (tp40) cc_final: 0.7908 (mm110)
  outliers start: 46
  outliers final: 24
  residues processed: 112
  average time/residue: 1.3963
  time to fit residues: 166.6341
Evaluate side-chains
  110 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 77
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  988 LYS
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Chi-restraints excluded: chain A residue 1347 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0870
   chunk 74 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 59 optimal weight:   30.0000
   chunk 51 optimal weight:   30.0000
   chunk 80 optimal weight:    0.8980
   chunk 17 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.1560

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 830 GLN
A 963 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.181298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.107062 restraints weight = 8162.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 3.63
r_work: 0.2991 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8548  Z= 0.153
  Angle     :  0.580   8.502  11613  Z= 0.291
  Chirality :  0.040   0.195   1368
  Planarity :  0.005   0.050   1440
  Dihedral  :  9.562  87.485   1264
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 21.34 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.27), residues: 1030
  helix:  2.60 (0.22), residues: 551
  sheet:  0.24 (0.45), residues: 115
  loop : -0.15 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A1253 
 PHE   0.018   0.001   PHE A1093 
 TYR   0.012   0.001   TYR A 312 
 ARG   0.002   0.000   ARG A 380 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00767 (    2)
  link_NAG-ASN         : angle       1.90376 (    6)
  link_BETA1-4         : bond        0.00465 (    2)
  link_BETA1-4         : angle       2.16652 (    6)
  hydrogen bonds       : bond        0.07734 (  467)
  hydrogen bonds       : angle       4.08174 ( 1350)
  covalent geometry    : bond        0.00339 ( 8544)
  covalent geometry    : angle       0.57675 (11601)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 82
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6191 (ttmt)
REVERT: A   78 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8013 (mp)
REVERT: A  344 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7471 (mtp180)
REVERT: A  754 MET cc_start: 0.1049 (tpt) cc_final: 0.0825 (tpp)
REVERT: A 1000 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8301 (mp)
REVERT: A 1053 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7778 (pt0)
REVERT: A 1225 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7832 (m-80)
REVERT: A 1260 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7433 (mtp85)
REVERT: A 1288 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7896 (mp)
REVERT: A 1294 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7536 (mmp80)
  outliers start: 43
  outliers final: 20
  residues processed: 111
  average time/residue: 1.5014
  time to fit residues: 177.3894
Evaluate side-chains
  111 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  988 LYS
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Chi-restraints excluded: chain A residue 1347 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    0.4980
   chunk 62 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0010
   chunk 85 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 52 optimal weight:   20.0000
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.6388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.182720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.110311 restraints weight = 8153.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 3.77
r_work: 0.3008 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.1088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8548  Z= 0.127
  Angle     :  0.533   8.060  11613  Z= 0.270
  Chirality :  0.038   0.174   1368
  Planarity :  0.004   0.050   1440
  Dihedral  :  9.240  88.277   1262
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 21.56 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.27), residues: 1030
  helix:  2.81 (0.22), residues: 544
  sheet:  0.23 (0.45), residues: 112
  loop : -0.08 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A1253 
 PHE   0.014   0.001   PHE A1093 
 TYR   0.014   0.001   TYR A 551 
 ARG   0.003   0.000   ARG A 380 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00719 (    2)
  link_NAG-ASN         : angle       1.93234 (    6)
  link_BETA1-4         : bond        0.00341 (    2)
  link_BETA1-4         : angle       2.14052 (    6)
  hydrogen bonds       : bond        0.06624 (  467)
  hydrogen bonds       : angle       3.94485 ( 1350)
  covalent geometry    : bond        0.00256 ( 8544)
  covalent geometry    : angle       0.52966 (11601)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 81
  time to evaluate  : 1.969 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6402 (ttmt)
REVERT: A   78 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8352 (mp)
REVERT: A  344 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7719 (mtp180)
REVERT: A  403 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8391 (mp)
REVERT: A  555 MET cc_start: 0.4419 (ppp) cc_final: 0.4154 (ppp)
REVERT: A 1000 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8380 (mp)
REVERT: A 1225 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7796 (m-80)
REVERT: A 1260 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7674 (mtp85)
REVERT: A 1288 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8176 (mp)
REVERT: A 1294 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7633 (mmp80)
  outliers start: 41
  outliers final: 20
  residues processed: 110
  average time/residue: 1.7849
  time to fit residues: 209.3810
Evaluate side-chains
  108 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  988 LYS
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Chi-restraints excluded: chain A residue 1347 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 45 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.180541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.107515 restraints weight = 8221.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 3.60
r_work: 0.2985 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8548  Z= 0.163
  Angle     :  0.599   9.134  11613  Z= 0.301
  Chirality :  0.041   0.184   1368
  Planarity :  0.005   0.050   1440
  Dihedral  :  9.266  89.989   1260
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 21.88 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.27), residues: 1030
  helix:  2.56 (0.22), residues: 551
  sheet:  0.24 (0.44), residues: 115
  loop : -0.18 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1310 
 HIS   0.003   0.001   HIS A1253 
 PHE   0.020   0.001   PHE A1093 
 TYR   0.013   0.001   TYR A 993 
 ARG   0.003   0.000   ARG A 380 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00717 (    2)
  link_NAG-ASN         : angle       1.48556 (    6)
  link_BETA1-4         : bond        0.00321 (    2)
  link_BETA1-4         : angle       2.12519 (    6)
  hydrogen bonds       : bond        0.08095 (  467)
  hydrogen bonds       : angle       4.05409 ( 1350)
  covalent geometry    : bond        0.00365 ( 8544)
  covalent geometry    : angle       0.59676 (11601)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 83
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6565 (tmmt)
REVERT: A   78 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7930 (mp)
REVERT: A  195 GLU cc_start: 0.8756 (tt0) cc_final: 0.8274 (tt0)
REVERT: A  344 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7496 (mtp180)
REVERT: A  428 SER cc_start: 0.7577 (t) cc_final: 0.7306 (p)
REVERT: A  555 MET cc_start: 0.4414 (ppp) cc_final: 0.4139 (ppp)
REVERT: A 1000 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8252 (mp)
REVERT: A 1087 TYR cc_start: 0.6699 (t80) cc_final: 0.6337 (t80)
REVERT: A 1225 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7817 (m-80)
REVERT: A 1260 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7395 (mtp85)
REVERT: A 1294 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7447 (mmp80)
  outliers start: 39
  outliers final: 26
  residues processed: 112
  average time/residue: 1.3455
  time to fit residues: 160.9213
Evaluate side-chains
  113 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  988 LYS
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Chi-restraints excluded: chain A residue 1318 VAL
Chi-restraints excluded: chain A residue 1347 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 60 optimal weight:   30.0000
   chunk 27 optimal weight:    0.4980
   chunk 81 optimal weight:    0.5980
   chunk 96 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.185022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.115067 restraints weight = 8186.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.89
r_work: 0.3084 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8548  Z= 0.133
  Angle     :  0.561   9.864  11613  Z= 0.282
  Chirality :  0.039   0.193   1368
  Planarity :  0.005   0.050   1440
  Dihedral  :  9.079  89.628   1260
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 21.56 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.27), residues: 1030
  helix:  2.71 (0.22), residues: 550
  sheet:  0.27 (0.44), residues: 115
  loop : -0.14 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A1253 
 PHE   0.014   0.001   PHE A1093 
 TYR   0.010   0.001   TYR A 312 
 ARG   0.003   0.000   ARG A 380 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00788 (    2)
  link_NAG-ASN         : angle       1.39874 (    6)
  link_BETA1-4         : bond        0.00333 (    2)
  link_BETA1-4         : angle       2.08007 (    6)
  hydrogen bonds       : bond        0.06940 (  467)
  hydrogen bonds       : angle       4.00172 ( 1350)
  covalent geometry    : bond        0.00269 ( 8544)
  covalent geometry    : angle       0.55793 (11601)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 80
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6417 (ttmt)
REVERT: A   78 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8349 (mp)
REVERT: A  344 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7709 (mtp180)
REVERT: A  555 MET cc_start: 0.4381 (ppp) cc_final: 0.4109 (ppp)
REVERT: A 1000 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8335 (mp)
REVERT: A 1087 TYR cc_start: 0.7072 (t80) cc_final: 0.6500 (t80)
REVERT: A 1225 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7826 (m-80)
REVERT: A 1260 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7634 (mtp85)
REVERT: A 1288 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8130 (mp)
REVERT: A 1294 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7600 (mmp80)
  outliers start: 42
  outliers final: 28
  residues processed: 110
  average time/residue: 1.3201
  time to fit residues: 154.7054
Evaluate side-chains
  113 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 77
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  988 LYS
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Chi-restraints excluded: chain A residue 1318 VAL
Chi-restraints excluded: chain A residue 1347 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 95 optimal weight:    0.0870
   chunk 102 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 83 optimal weight:    0.2980
   chunk 67 optimal weight:    0.0370
   chunk 48 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0050
   chunk 70 optimal weight:    0.9990
   chunk 75 optimal weight:    0.2980
   overall best weight:    0.1450

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 426 ASN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.190213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.120937 restraints weight = 8342.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 3.13
r_work: 0.3189 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8548  Z= 0.116
  Angle     :  0.536   9.939  11613  Z= 0.267
  Chirality :  0.038   0.203   1368
  Planarity :  0.004   0.051   1440
  Dihedral  :  8.692  86.936   1260
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 22.63 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.27), residues: 1030
  helix:  3.04 (0.23), residues: 541
  sheet:  0.05 (0.45), residues: 118
  loop :  0.16 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 310 
 HIS   0.004   0.000   HIS A 208 
 PHE   0.011   0.001   PHE A 716 
 TYR   0.008   0.001   TYR A 551 
 ARG   0.003   0.000   ARG A 380 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01688 (    2)
  link_NAG-ASN         : angle       2.90051 (    6)
  link_BETA1-4         : bond        0.00368 (    2)
  link_BETA1-4         : angle       2.59951 (    6)
  hydrogen bonds       : bond        0.05133 (  467)
  hydrogen bonds       : angle       3.83950 ( 1350)
  covalent geometry    : bond        0.00220 ( 8544)
  covalent geometry    : angle       0.52855 (11601)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 81
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6342 (ttmt)
REVERT: A   78 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8176 (mp)
REVERT: A  403 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8219 (mp)
REVERT: A  555 MET cc_start: 0.4401 (ppp) cc_final: 0.4122 (ppp)
REVERT: A 1087 TYR cc_start: 0.6736 (t80) cc_final: 0.6162 (t80)
REVERT: A 1225 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7130 (m-80)
REVERT: A 1260 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7624 (mtp85)
REVERT: A 1294 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7616 (mmp80)
  outliers start: 34
  outliers final: 14
  residues processed: 106
  average time/residue: 1.2939
  time to fit residues: 146.2681
Evaluate side-chains
  98 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1294 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 64 optimal weight:    0.0030
   chunk 101 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 102 optimal weight:    0.7980
   chunk 50 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.9194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 ASN
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.185445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.115823 restraints weight = 8189.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 3.64
r_work: 0.3091 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8548  Z= 0.140
  Angle     :  0.579  10.525  11613  Z= 0.289
  Chirality :  0.040   0.234   1368
  Planarity :  0.004   0.049   1440
  Dihedral  :  8.210  82.927   1252
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.05 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.27), residues: 1030
  helix:  2.94 (0.23), residues: 541
  sheet:  0.30 (0.45), residues: 113
  loop :  0.05 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  67 
 HIS   0.003   0.001   HIS A1253 
 PHE   0.019   0.001   PHE A1093 
 TYR   0.011   0.001   TYR A 993 
 ARG   0.003   0.000   ARG A 380 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01349 (    2)
  link_NAG-ASN         : angle       2.53961 (    6)
  link_BETA1-4         : bond        0.00400 (    2)
  link_BETA1-4         : angle       2.09235 (    6)
  hydrogen bonds       : bond        0.06896 (  467)
  hydrogen bonds       : angle       3.91743 ( 1350)
  covalent geometry    : bond        0.00302 ( 8544)
  covalent geometry    : angle       0.57408 (11601)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6372 (ttmt)
REVERT: A   78 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8387 (mp)
REVERT: A  555 MET cc_start: 0.4425 (ppp) cc_final: 0.4136 (ppp)
REVERT: A  700 MET cc_start: 0.2900 (OUTLIER) cc_final: 0.1993 (ptp)
REVERT: A 1087 TYR cc_start: 0.7155 (t80) cc_final: 0.6491 (t80)
REVERT: A 1225 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7654 (m-80)
REVERT: A 1260 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7670 (mtp85)
REVERT: A 1294 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7661 (mmp80)
  outliers start: 28
  outliers final: 20
  residues processed: 100
  average time/residue: 1.3270
  time to fit residues: 141.3102
Evaluate side-chains
  103 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  700 MET
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1127 LEU
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 96 optimal weight:    0.0980
   chunk 61 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 52 optimal weight:   20.0000
   chunk 50 optimal weight:    9.9990
   chunk 91 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0980
   chunk 94 optimal weight:    0.7980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.186737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.118058 restraints weight = 8336.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 3.85
r_work: 0.3121 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8548  Z= 0.124
  Angle     :  0.557  10.264  11613  Z= 0.278
  Chirality :  0.039   0.222   1368
  Planarity :  0.004   0.050   1440
  Dihedral  :  8.134  82.503   1252
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 23.27 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.27), residues: 1030
  helix:  2.98 (0.23), residues: 541
  sheet:  0.33 (0.45), residues: 113
  loop :  0.09 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A1253 
 PHE   0.013   0.001   PHE A1093 
 TYR   0.009   0.001   TYR A 312 
 ARG   0.003   0.000   ARG A 380 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01324 (    2)
  link_NAG-ASN         : angle       2.74735 (    6)
  link_BETA1-4         : bond        0.00392 (    2)
  link_BETA1-4         : angle       2.10603 (    6)
  hydrogen bonds       : bond        0.06254 (  467)
  hydrogen bonds       : angle       3.88947 ( 1350)
  covalent geometry    : bond        0.00248 ( 8544)
  covalent geometry    : angle       0.55147 (11601)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8483.87 seconds
wall clock time: 147 minutes 40.54 seconds (8860.54 seconds total)